PDB

Protein Data Bank

l A repository for 3-D biological macromolecular

structure

l All data are available to the public

l It includes proteins, nucleic acids and viruses

l Obtained by X-Ray crystallography (80%) or

NMR spectroscopy (16%)

l Submitted by biologists and biochemists from

around the world

l PDB is an important resource for research in the

academic, pharmaceutical, and biotechnology

sectors

l Examples

– Will this molecule turns into a cancer cell?

– Can this combination of molecules cure common cold?

– How does radiation affect the RNA and DNA?

PDB data

l Information required includes

– Coordinates of all the atoms

– Chemical description of the various molecules

in the crystal

– Experimental information about the structure

– Structural description of the biological molecule

Software Tools

l Various software tools can minimize the

amount of manual labor

l Help scientists deposit their results quicker

l Also help validate their results

l Commonly used software:

– pdb_extract

– ADIT

– PDB Validation Suite

Some examples :

 

 

Trypsin(STRUCTURE OF FORM III CRYSTALS OF BOVINE PANCREATIC TRYPSIN INHIBITOR)

Classification:	Proteinase Inhibitor (trypsin)
Structure Weight:	6622.57

Molecule:

PANCREATIC TRYPSIN INHIBITOR PRECURSOR

Polymer:

1

Type:

protein

Length:

58

Chains:

A

Organism

Bos taurus

Amylase(ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE)

Classification:	Alpha Amylase
Structure Weight:	48016.77

Molecule:

ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE

Polymer:

1

Type:

protein

Length:

425

Chains:

A

EC#:

3.2.1.1

Mutation:

E208Q

Details:

COMPLEXED WITH MALTOPENTAOSE

Organism

Bacillus subtilis

Gene Names

amyE amyA BSU03040

 

 

 

Pepsin(X-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUCTURE OF THE HEXAGONAL CRYSTAL FORM OF PORCINE PEPSIN AT 2.3 ANGSTROMS RESOLUTION)

Classification:	Hydrolase(acid Proteinase)
Structure Weight:	34469.80

Molecule:

PEPSIN

Polymer:

1

Type:

protein

Length:

326

Chains:

A

EC#:

3.4.23.1

Organism

Sus scrofa

Gene Name

PGA

Htra(Solution structure of HtrA PDZ domain from Streptococcus pneumoniae)

Classification:	Protein Binding
Structure Weight:	14890.90

Molecule:

Putative serine protease

Polymer:

1

Type:

protein

Length:

134

Chains:

A

Fragment:

PDZ domain, UNP residues 266-390

Organism

Streptococcus pneumoniae

Gene Name

SP_2239

Carboxypeptidase(CRYSTAL STRUCTURE OF BOVINE PANCREATIC CARBOXYPEPTIDASE A COMPLEXED WITH AMINOCARBONYLPHENYLALANINE AT 1.75 A)

Classification:	Carboxypeptidase
Structure Weight:	138865.59

Molecule:

CARBOXYPEPTIDASE A

Polymer:

1

Type:

protein

Length:

307

Chains:

A, B, D, E

EC#:

3.4.17.1

Organism

Bos taurus

Gene Names

CPA1 CPA

SMILES!

     No, not that kind of smile, but SMILES as in Simplified molecular-input line entry system. It is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII (American Standard Code for Information Interchange) strings. It can be imported by various molecule editors. For this post, we focus on or use Chemsketch as our molecule editor. It is quite nice I must say. So far. To put in a simpler manner, it is how to draw 2D molecular structure in skeletal form with notation to make it easier to read and understand

     To know more, please kindly click on this link and it will take you to wikipedia on more detailed description for the SMILES. Also, a little bit about the molecule editor. It is a computer program for creating and modifying representations of chemical structures. It can either manipulate it in 2D and 3D. Here's some links to some cool molecular editor.(Which are free! Or at least freeware is available.)

ACD/Chemsketch	http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
Accelrys Draw	http://accelrys.com/products/informatics/cheminformatics/draw/index.html

Now, back to SMILES. Here are some pictures of the chemical molecular structures. All of them were drawn using Chemsketch. Notice the wordings below the structure are called SMILES notation